African Soil Microbiology Project

written by Elizabeth Bach, Executive Director, Global Soil Biodiversity Initiative


Of all the continents, Africa faces the largest challenges concerning soil conservation and food security, in the face of increasing populations and environmental change.

Scientists from several sub-Saharan African countries including South Africa, Namibia, Mozambique, Kenya, Botswana and Zambia met recently at the University of Pretoria to launch the African Soil Microbiology Project (AfSM), funded by USAID.

Over 3-years, soil samples will be collected methodically across the continent of Africa.  Using the Earth Microbiome standard methodology, soil samples will be analyzed in the laboratories of the collaborating scientists to extract DNA, amplify and sequence the 16S rDNA gene, and analyze matches to known bacterial and archaeal taxa.  This unique multi-national project is the first such study to ever be undertaken in Africa at this scale.

“AfSM is a consortium of soil microbiology researchers from across sub-Saharan Africa, representing about 15% of the total land area of the region.  The core project will involve a coordinated assessment program of collecting 1000 soil samples across each of the partner nations for microbial community fingerprinting,” said Dr. Diana Wall, an International Advisor to the project.

Results from the project will shed new light on the bacterial biodiversity of African soils.  It will provide new insights into the presence of beneficial and pathogenic bacteria.  Knowing the distribution of key groups of bacteria, such as nitrogen-fixing Rhizobium and Azotobacter, may provide new information for land use and crop management decision-making.  Uncovering the ecology of these soil communities may provide new ideas for managing pathogens of crop plants, livestock, wildlife, and humans.  The data and collaborations will serve as foundations for future explorations of microbial soil biodiversity in Africa.

For more information, contact the project director, Prof Don Cowan (

The African Soil Microbiology project team, in the Centre of Microbial
Ecology and Genomics laboratories at the University of Pretoria, South Africa.